cleanup and formatting fix

doc/install.rst

@@ -150,7 +150,7 @@ Tuberculosis multilabel dataset
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 
 The following dataset contains the labels healthy, sick & non-TB, active TB,
-and latent TB. The implemented tbx11k dataset in this package is based on 
+and latent TB. The implemented tbx11k dataset in this package is based on
 the simplified version, which is just a more compact version of the original.
 In addition to the splits presented in the following table, 10 folds
 (for cross-validation) randomly generated are available for these datasets.

doc/references.rst

@@ -60,12 +60,12 @@
    diagnosing HIV-Associated tuberculosis in an emergency center.**,
    J. Acquir. Immune Defic. Syndr. 1999 81, e10–e14 (2019).
 
-.. [TBX11K-2020] *Liu, Y., Wu, Y.-H., Ban, Y., Wang, H., and Cheng, M.-*, 
+.. [TBX11K-2020] *Liu, Y., Wu, Y.-H., Ban, Y., Wang, H., and Cheng, M.-*,
    **Rethinking computer-aided tuberculosis diagnosis.**,
    In Proceedings of the IEEE/CVF Conference on Computer Vision and Pattern
    Recognition, pages 2646–2655.
 
-.. [TBX11K-SIMPLIFIED-2020] *Liu, Y., Wu, Y.-H., Ban, Y., Wang, H., and Cheng, M.-*, 
+.. [TBX11K-SIMPLIFIED-2020] *Liu, Y., Wu, Y.-H., Ban, Y., Wang, H., and Cheng, M.-*,
    **Rethinking computer-aided tuberculosis diagnosis.**,
    In Proceedings of the IEEE/CVF Conference on Computer Vision and Pattern
    Recognition, pages 2646–2655.

src/ptbench/configs/datasets/tbx11k_simplified/__init__.py

@@ -7,7 +7,7 @@ def _maker(protocol, RGB=False):
     from torchvision import transforms
 
     from ....data.tbx11k_simplified import dataset as raw
-    from ....data.transforms import ElasticDeformation, RemoveBlackBorders, RGBtoGreyscale8bit
+    from ....data.transforms import ElasticDeformation, RGBtoGreyscale8bit
     from .. import make_dataset as mk
 
     post_transforms = []
@@ -19,9 +19,7 @@ def _maker(protocol, RGB=False):
 
     return mk(
         [raw.subsets(protocol)],
-        [
-            RGBtoGreyscale8bit()
-        ],
+        [RGBtoGreyscale8bit()],
         [ElasticDeformation(p=0.8)],
         post_transforms,
     )

src/ptbench/data/tbx11k_simplified/__init__.py

@@ -32,19 +32,21 @@ from ..loader import load_pil_baw, make_delayed
 
 _protocols = [
     importlib.resources.files(__name__).joinpath("default.json.bz2"),
-    #importlib.resources.files(__name__).joinpath("fold_0.json.bz2"),
-    #importlib.resources.files(__name__).joinpath("fold_1.json.bz2"),
-    #importlib.resources.files(__name__).joinpath("fold_2.json.bz2"),
-    #importlib.resources.files(__name__).joinpath("fold_3.json.bz2"),
-    #importlib.resources.files(__name__).joinpath("fold_4.json.bz2"),
-    #importlib.resources.files(__name__).joinpath("fold_5.json.bz2"),
-    #importlib.resources.files(__name__).joinpath("fold_6.json.bz2"),
-    #importlib.resources.files(__name__).joinpath("fold_7.json.bz2"),
-    #importlib.resources.files(__name__).joinpath("fold_8.json.bz2"),
-    #importlib.resources.files(__name__).joinpath("fold_9.json.bz2"),
+    # importlib.resources.files(__name__).joinpath("fold_0.json.bz2"),
+    # importlib.resources.files(__name__).joinpath("fold_1.json.bz2"),
+    # importlib.resources.files(__name__).joinpath("fold_2.json.bz2"),
+    # importlib.resources.files(__name__).joinpath("fold_3.json.bz2"),
+    # importlib.resources.files(__name__).joinpath("fold_4.json.bz2"),
+    # importlib.resources.files(__name__).joinpath("fold_5.json.bz2"),
+    # importlib.resources.files(__name__).joinpath("fold_6.json.bz2"),
+    # importlib.resources.files(__name__).joinpath("fold_7.json.bz2"),
+    # importlib.resources.files(__name__).joinpath("fold_8.json.bz2"),
+    # importlib.resources.files(__name__).joinpath("fold_9.json.bz2"),
 ]
 
-_datadir = load_rc().get("datadir.tbx11k_simplified", os.path.realpath(os.curdir))
+_datadir = load_rc().get(
+    "datadir.tbx11k_simplified", os.path.realpath(os.curdir)
+)
 
 
 def _raw_data_loader(sample):

src/ptbench/data/tbx11k_simplified_RS/__init__.py

@@ -2,8 +2,8 @@
 #
 # SPDX-License-Identifier: GPL-3.0-or-later
 
-"""Extended TBX11K simplified dataset for computer-aided diagnosis 
-(extended with DensenetRS predictions)
+"""Extended TBX11K simplified dataset for computer-aided diagnosis (extended
+with DensenetRS predictions)
 
 The TBX11K database has been established to foster research
 in computer-aided diagnosis of pulmonary diseases with a special
@@ -31,16 +31,16 @@ from ..loader import make_delayed
 
 _protocols = [
     importlib.resources.files(__name__).joinpath("default.json.bz2"),
-    #importlib.resources.files(__name__).joinpath("fold_0.json.bz2"),
-    #importlib.resources.files(__name__).joinpath("fold_1.json.bz2"),
-    #importlib.resources.files(__name__).joinpath("fold_2.json.bz2"),
-    #importlib.resources.files(__name__).joinpath("fold_3.json.bz2"),
-    #importlib.resources.files(__name__).joinpath("fold_4.json.bz2"),
-    #importlib.resources.files(__name__).joinpath("fold_5.json.bz2"),
-    #importlib.resources.files(__name__).joinpath("fold_6.json.bz2"),
-    #importlib.resources.files(__name__).joinpath("fold_7.json.bz2"),
-    #importlib.resources.files(__name__).joinpath("fold_8.json.bz2"),
-    #importlib.resources.files(__name__).joinpath("fold_9.json.bz2"),
+    # importlib.resources.files(__name__).joinpath("fold_0.json.bz2"),
+    # importlib.resources.files(__name__).joinpath("fold_1.json.bz2"),
+    # importlib.resources.files(__name__).joinpath("fold_2.json.bz2"),
+    # importlib.resources.files(__name__).joinpath("fold_3.json.bz2"),
+    # importlib.resources.files(__name__).joinpath("fold_4.json.bz2"),
+    # importlib.resources.files(__name__).joinpath("fold_5.json.bz2"),
+    # importlib.resources.files(__name__).joinpath("fold_6.json.bz2"),
+    # importlib.resources.files(__name__).joinpath("fold_7.json.bz2"),
+    # importlib.resources.files(__name__).joinpath("fold_8.json.bz2"),
+    # importlib.resources.files(__name__).joinpath("fold_9.json.bz2"),
 ]
 
 

src/ptbench/data/transforms.py

@@ -41,15 +41,16 @@ class SingleAutoLevel16to8:
             ).astype("uint8"),
         ).convert("L")
 
+
 class RGBtoGreyscale8bit:
     """Converts a 24-bit RGB image to an 8-bit greyscale representation.
-    
+
     This transform assumes that the input image is RGB with 24 bits.
 
     Converts the RGB image to a greyscale image using the well-known formula:
     Y = 0.299 * R + 0.587 * G + 0.114 * B
     This formula is based on the relative luminance of the RGB channels in the sRGB color space
-    
+
     consider such a range should be mapped to the [0,255] range of the
     destination image.
     """
@@ -57,14 +58,23 @@ class RGBtoGreyscale8bit:
     def __call__(self, img):
         # Use the formula to convert the RGB image to a greyscale image
         img_array = numpy.array(img).astype(float)
-        grey_array = 0.299 * img_array[:, :, 0] + 0.587 * img_array[:, :, 1] + 0.114 * img_array[:, :, 2]
-        
+        grey_array = (
+            0.299 * img_array[:, :, 0]
+            + 0.587 * img_array[:, :, 1]
+            + 0.114 * img_array[:, :, 2]
+        )
+
         # Normalize the greyscale image to the range [0, 255] and convert it to uint8
-        grey_array = numpy.round(255.0 * (grey_array - grey_array.min()) / (grey_array.max() - grey_array.min())).astype('uint8')
-        
+        grey_array = numpy.round(
+            255.0
+            * (grey_array - grey_array.min())
+            / (grey_array.max() - grey_array.min())
+        ).astype("uint8")
+
         # Create a new greyscale PIL image from the normalized array
         return PIL.Image.fromarray(grey_array).convert("L")
 
+
 class RemoveBlackBorders:
     """Remove black borders of CXR."""